The invention is designed to diagnose cardiovascular system (CVS) based on at least 148 quantitative ECG parameters including Heart Rate Variability (HRV) ones. Parameters are rated to 100 points, divided into 7 groups with close physiological nature, 4 diagnostic criteria (evaluation of CVS regulation, myocardium state, emotion state, HR disorders) and complex index of functional state (CIFS) are calculated. Aggregated diagnostic and prognostic decision are made about the functional CVS state and psycho-emotional state by combining CIFS, Hannover (or other similar algorithm), Minnesota code, myocardial abnormalities codes, and prediction codes of serious cardiovascular events. The method increases the accuracy and reliability of diagnostics.